soma-schema 0.2.2__tar.gz

soma_schema-0.2.2/.gitignore

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+# DataHarmonizer build artifacts
+node_modules/
+dist/
+docs/harmonizer.html
+docs/schemas/
+docs/menu.json
+docs/assets/
+
+# generated part of documentation
+/docs/elements/*.md
+/docs/artifacts/
+/docs/examples/
+/docs/schema/
+
+# docs copied from src/docs by justfile _copy-docs
+/docs/about.md
+/docs/artifacts.md
+/docs/examples.md
+/docs/index.md
+# linkml-run-examples output (not useful to have in git in its current form)
+/examples/output/
+
+# Derived schemas, generated from the schema.yaml
+tmp/
+project/*
+!project/README.md
+!project/excel/
+!project/sqlschema/
+!project/jsonschema/
+!project/owl/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pycharm
+.idea
+# Local vscode editor config
+.vscode

soma_schema-0.2.2/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2025 Sierra Moxon
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

soma_schema-0.2.2/PKG-INFO

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+Metadata-Version: 2.5
+Name: soma-schema
+Version: 0.2.2
+Summary: This is the project description.
+Author-email: Sierra Moxon <smoxon@lbl.gov>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: <4.0,>=3.9
+Requires-Dist: linkml-runtime>=1.9.4
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <img src="src/docs/soma-logo.svg" alt="SOMA Logo" width="700">
+</p>
+
+<p align="center">
+  A <a href="https://linkml.io/">LinkML</a> schema for representing Key Event and Outcome measurements, assays, and experimental protocols in the context of environmental health sciences (EHS) outcomes research.
+</p>
+
+<p align="center">
+  <a href="https://EHS-Data-Standards.github.io/soma"><strong>Documentation</strong></a> &middot;
+  <a href="https://EHS-Data-Standards.github.io/soma/elements/"><strong>Schema</strong></a> &middot;
+  <a href="https://EHS-Data-Standards.github.io/soma/examples.html"><strong>Examples</strong></a> &middot;
+  <a href="https://EHS-Data-Standards.github.io/soma/artifacts.html"><strong>Artifacts</strong></a>
+</p>
+
+---
+
+## Purpose
+
+This data model provides a standardized way to capture and exchange data about airway biology
+assays relevant to respiratory health outcomes, including:
+
+- **Ciliary function** - Beat frequency, active area, morphology
+- **Airway surface liquid** - ASL height, periciliary layer depth, ion composition
+- **Mucociliary clearance** - Transport rates, directionality, clearance efficiency
+- **Oxidative stress** - ROS, lipid peroxidation, antioxidant capacity
+- **Ion channel function** - CFTR chloride secretion, sweat chloride
+- **Signaling pathways** - EGFR phosphorylation, downstream kinases
+- **Mucin biology** - Goblet cells, MUC5AC/MUC5B expression
+- **Inflammatory markers** - BALF/sputum cell counts, cytokines
+- **Lung function** - Spirometry outcomes (FEV1, FVC)
+- **Gene expression** - Target gene mRNA levels
+
+## Key Features
+
+- **Assay-centric architecture** with domain-specific assay classes using named measurement slots
+- **StudySubject hierarchy** for describing biological systems: cell cultures, human/animal subjects, populations
+- **Typed protocol hierarchy**: ImagingProtocol, MolecularAssayProtocol, StainingProtocol, SpirometryProtocol
+- **AOP Framework integration**: KeyEvent and AdverseOutcomePathway classes with assay linkage
+- **Ontology-backed** entities mapped to GO, ChEBI, CL, UO, OBI, and other biomedical ontologies
+
+## Getting Started
+
+The schema can be used to:
+
+1. **Validate data** - Ensure your data conforms to the model
+2. **Generate code** - Create Python dataclasses, Pydantic models, JSON Schema
+3. **Transform data** - Convert between JSON, YAML, RDF, and other formats
+
+## Development Workflow
+
+For local development, use `uv` and `just` as the canonical entry points.
+The repository may contain underlying Python, npm, and LinkML commands, but contributors
+should treat the `just` recipes as the supported interface for routine setup, testing,
+and generation tasks.
+
+### Prerequisites
+
+- `uv` for Python environment and dependency management
+- `just` for repository task automation
+- `node` and `npm` for DataHarmonizer frontend builds
+
+### Setup
+
+Install the Python dependencies managed by the repo:
+
+```bash
+just install
+```
+
+### Common Commands
+
+- Run the full validation workflow: `just test`
+- Regenerate project artifacts: `just gen-project`
+- Regenerate schema documentation: `just gen-doc`
+- Build the DataHarmonizer assets: `just build-dh`
+- List all available recipes: `just --list`
+
+If you need to run a Python tool directly, prefer `uv run ...` so it executes inside the
+managed project environment.
+
+## Repository Structure
+
+* [docs/](docs/) - mkdocs-managed documentation
+* [examples/](examples/) - Examples of using the schema
+* [project/](project/) - project files (auto-generated, do not edit)
+* [src/soma/schema/](src/soma/schema) - LinkML schema (edit this)
+* [src/soma/datamodel/](src/soma/datamodel) - generated Python datamodel
+* [tests/](tests/) - Python tests
+
+## Developer Tools
+
+There are several pre-defined command-recipes available.
+They are written for the command runner [just](https://github.com/casey/just/). To list all pre-defined commands, run `just` or `just --list`.
+
+## Credits
+
+This project uses the template [linkml-project-copier](https://github.com/dalito/linkml-project-copier) published as [doi:10.5281/zenodo.15163584](https://doi.org/10.5281/zenodo.15163584).

soma_schema-0.2.2/README.md

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+<p align="center">
+  <img src="src/docs/soma-logo.svg" alt="SOMA Logo" width="700">
+</p>
+
+<p align="center">
+  A <a href="https://linkml.io/">LinkML</a> schema for representing Key Event and Outcome measurements, assays, and experimental protocols in the context of environmental health sciences (EHS) outcomes research.
+</p>
+
+<p align="center">
+  <a href="https://EHS-Data-Standards.github.io/soma"><strong>Documentation</strong></a> &middot;
+  <a href="https://EHS-Data-Standards.github.io/soma/elements/"><strong>Schema</strong></a> &middot;
+  <a href="https://EHS-Data-Standards.github.io/soma/examples.html"><strong>Examples</strong></a> &middot;
+  <a href="https://EHS-Data-Standards.github.io/soma/artifacts.html"><strong>Artifacts</strong></a>
+</p>
+
+---
+
+## Purpose
+
+This data model provides a standardized way to capture and exchange data about airway biology
+assays relevant to respiratory health outcomes, including:
+
+- **Ciliary function** - Beat frequency, active area, morphology
+- **Airway surface liquid** - ASL height, periciliary layer depth, ion composition
+- **Mucociliary clearance** - Transport rates, directionality, clearance efficiency
+- **Oxidative stress** - ROS, lipid peroxidation, antioxidant capacity
+- **Ion channel function** - CFTR chloride secretion, sweat chloride
+- **Signaling pathways** - EGFR phosphorylation, downstream kinases
+- **Mucin biology** - Goblet cells, MUC5AC/MUC5B expression
+- **Inflammatory markers** - BALF/sputum cell counts, cytokines
+- **Lung function** - Spirometry outcomes (FEV1, FVC)
+- **Gene expression** - Target gene mRNA levels
+
+## Key Features
+
+- **Assay-centric architecture** with domain-specific assay classes using named measurement slots
+- **StudySubject hierarchy** for describing biological systems: cell cultures, human/animal subjects, populations
+- **Typed protocol hierarchy**: ImagingProtocol, MolecularAssayProtocol, StainingProtocol, SpirometryProtocol
+- **AOP Framework integration**: KeyEvent and AdverseOutcomePathway classes with assay linkage
+- **Ontology-backed** entities mapped to GO, ChEBI, CL, UO, OBI, and other biomedical ontologies
+
+## Getting Started
+
+The schema can be used to:
+
+1. **Validate data** - Ensure your data conforms to the model
+2. **Generate code** - Create Python dataclasses, Pydantic models, JSON Schema
+3. **Transform data** - Convert between JSON, YAML, RDF, and other formats
+
+## Development Workflow
+
+For local development, use `uv` and `just` as the canonical entry points.
+The repository may contain underlying Python, npm, and LinkML commands, but contributors
+should treat the `just` recipes as the supported interface for routine setup, testing,
+and generation tasks.
+
+### Prerequisites
+
+- `uv` for Python environment and dependency management
+- `just` for repository task automation
+- `node` and `npm` for DataHarmonizer frontend builds
+
+### Setup
+
+Install the Python dependencies managed by the repo:
+
+```bash
+just install
+```
+
+### Common Commands
+
+- Run the full validation workflow: `just test`
+- Regenerate project artifacts: `just gen-project`
+- Regenerate schema documentation: `just gen-doc`
+- Build the DataHarmonizer assets: `just build-dh`
+- List all available recipes: `just --list`
+
+If you need to run a Python tool directly, prefer `uv run ...` so it executes inside the
+managed project environment.
+
+## Repository Structure
+
+* [docs/](docs/) - mkdocs-managed documentation
+* [examples/](examples/) - Examples of using the schema
+* [project/](project/) - project files (auto-generated, do not edit)
+* [src/soma/schema/](src/soma/schema) - LinkML schema (edit this)
+* [src/soma/datamodel/](src/soma/datamodel) - generated Python datamodel
+* [tests/](tests/) - Python tests
+
+## Developer Tools
+
+There are several pre-defined command-recipes available.
+They are written for the command runner [just](https://github.com/casey/just/). To list all pre-defined commands, run `just` or `just --list`.
+
+## Credits
+
+This project uses the template [linkml-project-copier](https://github.com/dalito/linkml-project-copier) published as [doi:10.5281/zenodo.15163584](https://doi.org/10.5281/zenodo.15163584).

soma_schema-0.2.2/pyproject.toml

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+[build-system]
+requires = ["hatchling", "uv-dynamic-versioning"]
+build-backend = "hatchling.build"
+
+[project]
+name = "soma-schema"
+description = "This is the project description."
+authors = [
+  {name = "Sierra Moxon", email = "smoxon@lbl.gov"},
+]
+license = "MIT"
+license-files = ["LICENSE"]
+readme = "README.md"
+requires-python = ">=3.9,<4.0"
+dynamic = ["version"]
+
+dependencies = [
+  "linkml-runtime >=1.9.4",
+]
+
+[dependency-groups]
+dev = [
+    "linkml>=1.9.3",
+    "mkdocs-material>=8.2.8",
+    "mkdocs-mermaid2-plugin>=1.1.1",
+    "jupyter>=1.0.0",
+    "mknotebooks>= 0.8.0",
+    "oaklib>=0.6.0",
+]
+
+# See https://hatch.pypa.io/latest/config/build/#file-selection for how to
+# explicitly include files other than default into the build distributions.
+
+[tool.hatch.build.targets.sdist]
+# Without this, hatchling packs the whole repo (200+ MB of example PDFs)
+# and the upload exceeds PyPI's 100 MB file limit.
+only-include = ["src"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/soma"]
+
+[tool.hatch.version]
+source = "uv-dynamic-versioning"
+
+# Ref.: https://github.com/ninoseki/uv-dynamic-versioning/
+[tool.uv-dynamic-versioning]
+vcs = "git"
+style = "pep440"
+fallback-version = "0.0.0"
+
+# Ref.: https://docs.pytest.org/en/stable/reference/reference.html#configuration-options
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+# Ref.: https://github.com/codespell-project/codespell
+[tool.codespell]
+skip = [
+  "LICENSE",
+  "pyproject.toml",
+  "uv.lock",
+  "project/*",
+  "src/soma/datamodel/soma_pydantic.py",
+  "src/soma/datamodel/soma.py",
+]
+
+# Reminder: words have to be lowercased for the ignore-words-list
+ignore-words-list = "linke"
+quiet-level = 3
+
+# Ref.: https://github.com/crate-ci/typos (spell checker)
+[tool.typos.default.extend-words]
+linke = "linke"
+[tool.typos.files]
+extend-exclude = [
+  "LICENSE",
+  "uv.lock",
+  "pyproject.toml",
+  "project/*",
+  "src/soma/datamodel/soma_pydantic.py",
+  "src/soma/datamodel/soma.py",
+]

soma_schema-0.2.2/src/docs/about.md

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+# About
+
+## The SOMA
+
+The SOMA is part of the [EHS Data Standards](https://github.com/EHS-Data-Standards)
+initiative, focused on developing standardized data models for environmental health sciences research.
+
+## Project Goals
+
+This project aims to:
+
+1. **Standardize data representation** for exposure-outcome relationships in EHS research
+2. **Enable data interoperability** across studies, cohorts, and institutions
+3. **Support mechanistic understanding** through integration with Adverse Outcome Pathways (AOPs)
+4. **Bridge epidemiological and toxicological data** from human studies and model systems
+
+## The Data Model
+
+### Design Principles
+
+The SOMA follows these principles:
+
+- **Ontology-first** - All entities are mapped to established biomedical ontologies
+- **FAIR-compliant** - Supports Findable, Accessible, Interoperable, and Reusable data
+- **Extensible** - New assay types can be added without breaking existing data
+- **Multi-scale** - Captures data from molecular to population levels
+
+### Technology Stack
+
+The model is built using:
+
+- [LinkML](https://linkml.io/) - Linked Data Modeling Language for schema definition
+- [MkDocs](https://www.mkdocs.org/) with [Material theme](https://squidfunk.github.io/mkdocs-material/)
+  for documentation
+- Python for data validation and transformation
+
+### Core Domains
+
+| Domain | Description |
+|--------|-------------|
+| Assays | Domain-specific assay classes with named measurement slots (e.g., CiliaryFunctionAssay, LungFunctionAssay) |
+| Study Subjects | Biological systems under study: cell cultures (CellularSystem), human/animal subjects (InVivoSubject), populations (PopulationSubject) |
+| Protocols | Typed experimental procedures: ImagingProtocol, MolecularAssayProtocol, StainingProtocol, SpirometryProtocol |
+| AOP Framework | Adverse Outcome Pathways: KeyEvent, AdverseOutcomePathway, with assay linkage via `informs_on_key_event` |
+
+## Contributing
+
+We welcome contributions from the community. To contribute:
+
+1. Visit the [GitHub repository](https://github.com/EHS-Data-Standards/soma)
+2. Review the existing schema in `src/soma/schema/`
+3. Open an issue to discuss proposed changes
+4. Submit a pull request with your contributions
+
+## Development
+
+For local development, use [uv](https://docs.astral.sh/uv/) and
+[just](https://github.com/casey/just/) as the canonical entry points.
+The repository may contain underlying Python, npm, and LinkML commands, but
+contributors should treat the `just` recipes as the supported interface for
+routine setup, testing, and generation tasks.
+
+### Prerequisites
+
+- Python 3.10+
+- [uv](https://docs.astral.sh/uv/) for Python environment and dependency management
+- [just](https://github.com/casey/just/) for repository task automation
+- `node` and `npm` for DataHarmonizer frontend builds
+
+### Setup
+
+Install the Python dependencies managed by the repo:
+
+```bash
+just install
+```
+
+### Common Commands
+
+- Run the full validation workflow: `just test`
+- Regenerate project artifacts: `just gen-project`
+- Regenerate schema documentation: `just gen-doc`
+- Build the DataHarmonizer assets: `just build-dh`
+- Run the local documentation server: `just testdoc`
+- List all available recipes: `just --list`
+
+If you need to run a Python tool directly, prefer `uv run ...` so it executes
+inside the managed project environment.
+
+### Project Structure
+
+```
+soma/
+├── src/
+│   ├── docs/                    # Documentation source files
+│   └── soma/
+│       ├── schema/              # LinkML schema definition
+│       └── datamodel/           # Generated Python models
+├── docs/
+│   └── elements/                # Generated schema docs
+├── project/                     # Generated artifacts
+├── tests/
+│   └── data/                    # Test data files
+└── examples/                    # Usage examples
+```
+
+## License
+
+This project is released under the [MIT License](https://opensource.org/licenses/MIT).
+
+## Acknowledgments
+
+This project uses the [linkml-project-copier](https://github.com/dalito/linkml-project-copier)
+template for project structure and build tooling.
+
+## Contact
+
+For questions or feedback, please open an issue on the
+[GitHub repository](https://github.com/EHS-Data-Standards/soma/issues).

soma_schema-0.2.2/src/docs/artifacts.md

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+# Generated Artifacts
+
+Download the generated model serializations:
+
+- [JSON Schema](artifacts/soma.schema.json)
+- [Pydantic Model](artifacts/soma_pydantic.py)
+- [Python Dataclasses](artifacts/soma.py)
+- [Excel Spreadsheet](artifacts/soma.xlsx)
+
+## Paper-Derived SOMA Data
+
+SOMA-conformant data extracted from published PM2.5 research papers. Each workbook contains
+assay measurements mapped to the SOMA schema with full provenance (figure/table references,
+p-values, protocols, exposure conditions).
+
+### Montgomery et al. (2020)
+
+**"Genome-Wide Analysis Reveals Mucociliary Remodeling of the Nasal Airway Epithelium Induced by Urban PM2.5"**
+
+Am J Respir Cell Mol Biol. 2020;63(2):172-184 |
+[Paper](https://academic.oup.com/ajrcmb/article/63/2/172/8461239) |
+[PubMed Central](https://pmc.ncbi.nlm.nih.gov/articles/PMC7397762/) |
+DOI: 10.1165/rcmb.2019-0454OC
+
+- [Excel Workbook](artifacts/Montgomery2020_PM25_Mucociliary_SOMA.xlsx)
+- SOMA assay types: GeneExpressionAssay, GobletCellAssay, FoxJExpressionAssay
+- Key findings: CYP1A1 LFC=6.21 (AhR activation), MUC5AC+ cells FC=2.88, FOXJ1+ nuclei 75% decrease, 424 DEGs at moderate dose
+
+### Liu et al. (2024)
+
+**"PM2.5 Exposure Inhibits Transepithelial Anion Short-circuit Current by Downregulating P2Y2 Receptor/CFTR Pathway"**
+
+Int J Med Sci. 2024;21(10):1929-1944 |
+[Paper](https://www.medsci.org/v21p1929.htm) |
+DOI: 10.7150/ijms.96777
+
+- [Excel Workbook](artifacts/Liu2024_PM25_CFTR_SOMA.xlsx)
+- SOMA assay types: CFTRFunctionAssay, GeneExpressionAssay, GobletCellAssay, BALFSputumAssay, LungFunctionAssay
+- Key findings: PM2.5 downregulates P2Y2R/CFTR (p<0.05), inhibits Isc, increases goblet cells (p<0.001), elevates Th2 cytokines